From the journal:

Natural Product Reports

Scalability of mass spectrometry-based metabolomics for natural extracts libraries exploration: current status, challenges, and opportunities

Adriano Rutz, ORCID logo *a   Wout Bittremieux,b   Robin Schmid,cd   Olivier Cailloux, ORCID logo e   Justin J. J. van der Hooft ORCID logo fg  and  Mehdi A. Beniddir ORCID logo *h  

* Corresponding authors

a Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
E-mail: rutz@imsb.biol.ethz.ch

b Department of Computer Science, University of Antwerp, Antwerp, Belgium

c Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czechia

d mzio GmbH, Bremen, Germany

e LAMSADE, CNRS, Université Paris-Dauphine, Université PSL, 75016 Paris, France

f Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands

g Department of Biochemistry, University of Johannesburg, Johannesburg 2006, South Africa

h Université Paris-Saclay, CNRS, BioCIS, 17 Avenue des Sciences, 91400 Orsay, France
E-mail: mehdi.beniddir@universite-paris-saclay.fr

Abstract

Covering: up to 2025

This review explores the potential of bioinformatics and chemoinformatics tools to advance the exploration of natural extracts libraries (NELs). Although metabolomics has become a term used routinely in natural product (NP) research, the field remains focused on individual molecules or small sets of compounds, which restricts scalability. This narrow focus is mirrored in the computational handling of generated data, limiting broader insights. By challenging the traditional molecule-first paradigm—a framework historically shaped by practical constraints—we present our vision of using computational approaches to unlock the full potential of NELs, now and in the future.

Graphical abstract: Scalability of mass spectrometry-based metabolomics for natural extracts libraries exploration: current status, challenges, and opportunities

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Article information

DOI
https://doi.org/10.1039/D5NP00034C
Article type
Review Article
Submitted
01 May 2025
First published
15 Sep 2025
This article is Open Access
Creative Commons BY-NC license

Nat. Prod. Rep., 2025, Advance Article

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Scalability of mass spectrometry-based metabolomics for natural extracts libraries exploration: current status, challenges, and opportunities

A. Rutz, W. Bittremieux, R. Schmid, O. Cailloux, J. J. J. van der Hooft and M. A. Beniddir, Nat. Prod. Rep., 2025, Advance Article , DOI: 10.1039/D5NP00034C

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